From f96b513f23d608e7f3138875937c031f255f49c3 Mon Sep 17 00:00:00 2001 From: Andrey Alekseenko Date: Wed, 3 Nov 2021 06:47:25 +0000 Subject: [PATCH] Fix random typos --- api/legacy/include/gromacs/fileio/confio.h | 3 +- api/legacy/include/gromacs/math/functions.h | 4 +- .../analysis/radial-distribution-function.rst | 2 +- .../functions/polarization.rst | 2 +- src/gromacs/applied_forces/awh/biasstate.cpp | 6 ++- .../applied_forces/awh/correlationtensor.h | 6 ++- .../applied_forces/awh/histogramsize.h | 3 +- src/gromacs/domdec/gpuhaloexchange_impl.cu | 10 +++-- src/gromacs/ewald/pme_gpu_types_host_impl.h | 2 +- src/gromacs/gmxpreprocess/grompp.cpp | 2 +- src/gromacs/gpu_utils/cudautils.cuh | 3 +- src/gromacs/gpu_utils/gpuregiontimer.h | 6 ++- src/gromacs/gpu_utils/ocl_compiler.cpp | 5 ++- src/gromacs/mdlib/calc_verletbuf.h | 5 ++- src/gromacs/mdlib/coupling.h | 14 ++++--- src/gromacs/mdlib/sim_util.cpp | 3 +- .../state_propagator_data_gpu_impl_gpu.cpp | 2 +- src/gromacs/nbnxm/nbnxm.h | 37 ++++++++++--------- src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp | 3 +- src/gromacs/nbnxm/pairlist.cpp | 6 ++- .../pulling/transformationcoordinate.h | 3 +- src/gromacs/taskassignment/decidegpuusage.h | 3 +- 22 files changed, 77 insertions(+), 53 deletions(-) diff --git a/api/legacy/include/gromacs/fileio/confio.h b/api/legacy/include/gromacs/fileio/confio.h index bd69125d2e..f75b238fd5 100644 --- a/api/legacy/include/gromacs/fileio/confio.h +++ b/api/legacy/include/gromacs/fileio/confio.h @@ -141,7 +141,8 @@ void readConfAndAtoms(const char* infile, * \param[in,out] v Velocities will be stored when *v!=NULL * \param[out] box Box dimensions * \param[in] requireMasses Require masses to be present, either from tpr or from the mass - * database \returns if a topology is available + * database + * \returns if a topology is available */ gmx_bool read_tps_conf(const char* infile, struct t_topology* top, diff --git a/api/legacy/include/gromacs/math/functions.h b/api/legacy/include/gromacs/math/functions.h index af557fb6ad..9130522167 100644 --- a/api/legacy/include/gromacs/math/functions.h +++ b/api/legacy/include/gromacs/math/functions.h @@ -442,8 +442,8 @@ constexpr int64_t exactDiv(int64_t a, int64_t b) /*! \brief Round float to int * - * Rounding behavior is round to nearest. Rounding of halfway cases is implemention defined - * (either halway to even or halway away from zero). + * Rounding behavior is round to nearest. Rounding of halfway cases is implementation defined + * (either halfway to even or halfway away from zero). */ /* Implementation details: It is assumed that FE_TONEAREST is default and not changed by anyone. * Currently the implementation is using rint(f) because 1) on all known HW that is faster than diff --git a/docs/reference-manual/analysis/radial-distribution-function.rst b/docs/reference-manual/analysis/radial-distribution-function.rst index 0d106e488e..38be10c549 100644 --- a/docs/reference-manual/analysis/radial-distribution-function.rst +++ b/docs/reference-manual/analysis/radial-distribution-function.rst @@ -37,7 +37,7 @@ averaging is also performed in time. In practice the analysis program into spherical slices (from :math:`r` to :math:`r+dr`, see :numref:`Fig. %s ` A) and makes a histogram in stead of the :math:`\delta`-function. An example of the RDF of oxygen-oxygen in -SPC water \ :ref::ref:`80 ` is given in :numref:`Fig. %s ` +SPC water \ :ref:`80 ` is given in :numref:`Fig. %s ` .. _fig-rdf: diff --git a/docs/reference-manual/functions/polarization.rst b/docs/reference-manual/functions/polarization.rst index c332a3df56..ccdd526f5f 100644 --- a/docs/reference-manual/functions/polarization.rst +++ b/docs/reference-manual/functions/polarization.rst @@ -68,7 +68,7 @@ Thole polarization Based on early work by Thole :ref:`95 `, Roux and coworkers have implemented potentials for molecules like -ethanol \ :ref:`96 `\ :ref:`98 `. +ethanol \ :ref:`96 `, :ref:`98 `. Within such molecules, there are intra-molecular interactions between shell particles, however these must be screened because full Coulomb would be too strong. The potential between two shell particles :math:`i` diff --git a/src/gromacs/applied_forces/awh/biasstate.cpp b/src/gromacs/applied_forces/awh/biasstate.cpp index 7c8b1d0e2b..08fbd29a92 100644 --- a/src/gromacs/applied_forces/awh/biasstate.cpp +++ b/src/gromacs/applied_forces/awh/biasstate.cpp @@ -690,8 +690,10 @@ void mergeSharedUpdateLists(std::vector* updateList, * \param[in] grid The AWH bias. * \param[in] points The point state. * \param[in] originUpdatelist The origin of the rectangular region that has been sampled since - * last update. \param[in] endUpdatelist The end of the rectangular that has been sampled since - * last update. \param[in,out] updateList Local update list to set (assumed >= npoints long). + * last update. + * \param[in] endUpdatelist The end of the rectangular that has been sampled since + * last update. + * \param[in,out] updateList Local update list to set (assumed >= npoints long). */ void makeLocalUpdateList(const BiasGrid& grid, ArrayRef points, diff --git a/src/gromacs/applied_forces/awh/correlationtensor.h b/src/gromacs/applied_forces/awh/correlationtensor.h index 9da3928dc9..96f680428d 100644 --- a/src/gromacs/applied_forces/awh/correlationtensor.h +++ b/src/gromacs/applied_forces/awh/correlationtensor.h @@ -1,7 +1,8 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team. + * Copyright (c) 2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -251,7 +252,8 @@ public: * \param[in] weight The weight of the data. * \param[in] data One data point for each grid dimension. * \param[in] blockLengthInWeight If true, a block is measured in probability weight, otherwise - * in time. \param[in] t The simulation time. + * in time. + * \param[in] t The simulation time. */ void addData(double weight, gmx::ArrayRef data, bool blockLengthInWeight, double t); diff --git a/src/gromacs/applied_forces/awh/histogramsize.h b/src/gromacs/applied_forces/awh/histogramsize.h index f0c5725d33..7861e794bc 100644 --- a/src/gromacs/applied_forces/awh/histogramsize.h +++ b/src/gromacs/applied_forces/awh/histogramsize.h @@ -98,7 +98,8 @@ private: * \param[in] params The bias parameters. * \param[in] t Time. * \param[in] detectedCovering True if we detected that the sampling interval has been - * sufficiently covered. \param[in,out] weightsumCovering The weight sum for checking covering. + * sufficiently covered. + * \param[in,out] weightsumCovering The weight sum for checking covering. * \param[in,out] fplog Log file. * \returns the new histogram size. */ diff --git a/src/gromacs/domdec/gpuhaloexchange_impl.cu b/src/gromacs/domdec/gpuhaloexchange_impl.cu index 4a62a89532..f8950c13f6 100644 --- a/src/gromacs/domdec/gpuhaloexchange_impl.cu +++ b/src/gromacs/domdec/gpuhaloexchange_impl.cu @@ -100,9 +100,11 @@ __global__ void packSendBufKernel(float3* __restrict__ dataPacked, } /*! \brief unpack non-local force data buffer on the GPU using pre-populated "map" containing index - * information \param[out] data full array of force values \param[in] dataPacked packed - * array of force values to be transferred \param[in] map array of indices defining mapping - * from full to packed array \param[in] mapSize number of elements in map array + * information + * \param[out] data full array of force values + * \param[in] dataPacked packed array of force values to be transferred + * \param[in] map array of indices defining mapping from full to packed array + * \param[in] mapSize number of elements in map array */ template __global__ void unpackRecvBufKernel(float3* __restrict__ data, @@ -140,7 +142,7 @@ void GpuHaloExchange::Impl::reinitHalo(float3* d_coordinatesBuffer, float3* d_fo const gmx_domdec_comm_dim_t& cd = comm.cd[dimIndex_]; const gmx_domdec_ind_t& ind = cd.ind[pulse_]; - numHomeAtoms_ = comm.atomRanges.numHomeAtoms(); // offset for data recieved by this rank + numHomeAtoms_ = comm.atomRanges.numHomeAtoms(); // offset for data received by this rank // Determine receive offset for the dimension index and pulse of this halo exchange object int numZoneTemp = 1; diff --git a/src/gromacs/ewald/pme_gpu_types_host_impl.h b/src/gromacs/ewald/pme_gpu_types_host_impl.h index e1f7f17b90..69121ab07a 100644 --- a/src/gromacs/ewald/pme_gpu_types_host_impl.h +++ b/src/gromacs/ewald/pme_gpu_types_host_impl.h @@ -107,7 +107,7 @@ struct PmeGpuSpecific GpuEventSynchronizer syncSpreadGridD2H; /* Settings which are set at the start of the run */ - /*! \brief A boolean which tells whether the complex and real grids for cu/clFFT are different or same. Currenty true. */ + /*! \brief A boolean which tells whether the complex and real grids for cu/clFFT are different or same. Currently true. */ bool performOutOfPlaceFFT = false; /*! \brief A boolean which tells if the GPU timing events are enabled. * False by default, can be enabled by setting the environment variable GMX_ENABLE_GPU_TIMING. diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp index 4c9fbf8d93..899b5008c2 100644 --- a/src/gromacs/gmxpreprocess/grompp.cpp +++ b/src/gromacs/gmxpreprocess/grompp.cpp @@ -1577,7 +1577,7 @@ static bool haveDecoupledModeInMol(const gmx_moltype_t& molt, /*! \brief Checks if the Verlet buffer and constraint accuracy is sufficient for decoupled dynamic modes. * - * When decoupled modes are present and the accuray in insufficient, + * When decoupled modes are present and the accuracy in insufficient, * this routine issues a warning if the accuracy is insufficient. */ static void checkDecoupledModeAccuracy(const gmx_mtop_t* mtop, const t_inputrec* ir, warninp* wi) diff --git a/src/gromacs/gpu_utils/cudautils.cuh b/src/gromacs/gpu_utils/cudautils.cuh index 0c4507d809..f1f1c57cfc 100644 --- a/src/gromacs/gpu_utils/cudautils.cuh +++ b/src/gromacs/gpu_utils/cudautils.cuh @@ -272,7 +272,8 @@ std::array prepareGpuKernelArguments(KernelPtr kernel, * \param[in] deviceStream GPU stream to launch kernel in * \param[in] kernelName Human readable kernel description, for error handling only * \param[in] kernelArgs Array of the pointers to the kernel arguments, prepared by - * prepareGpuKernelArguments() \throws gmx::InternalError on kernel launch failure + * prepareGpuKernelArguments() + * \throws gmx::InternalError on kernel launch failure */ template void launchGpuKernel(void (*kernel)(Args...), diff --git a/src/gromacs/gpu_utils/gpuregiontimer.h b/src/gromacs/gpu_utils/gpuregiontimer.h index f0860b164d..a6614c1bba 100644 --- a/src/gromacs/gpu_utils/gpuregiontimer.h +++ b/src/gromacs/gpu_utils/gpuregiontimer.h @@ -1,7 +1,8 @@ /* * This file is part of the GROMACS molecular simulation package. * - * Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2016,2017,2018,2019,2020 by the GROMACS development team. + * Copyright (c) 2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -120,7 +121,8 @@ public: * Accumulates the last timespan of all the events used into the total duration, * and resets the internal timer state. * To be called after closeTimingRegion() and the command stream of the event having been - * synchronized. \returns The last timespan (in milliseconds). + * synchronized. + * \returns The last timespan (in milliseconds). */ double getLastRangeTime() { diff --git a/src/gromacs/gpu_utils/ocl_compiler.cpp b/src/gromacs/gpu_utils/ocl_compiler.cpp index 98b02df93a..5f826e5e0a 100644 --- a/src/gromacs/gpu_utils/ocl_compiler.cpp +++ b/src/gromacs/gpu_utils/ocl_compiler.cpp @@ -80,7 +80,7 @@ static bool useBuildCache = getenv("GMX_OCL_GENCACHE") != nullptr; /*! \brief Handles writing the OpenCL JIT compilation log to \c fplog. * - * If \c fplog is non-null and either the GMX_OCL_DUMP_LOG environment + * If \c fplog is non-null and either the \c GMX_OCL_DUMP_LOG environment * variable is set or the compilation failed, then the OpenCL * compilation log is written. * @@ -89,7 +89,8 @@ static bool useBuildCache = getenv("GMX_OCL_GENCACHE") != nullptr; * \param deviceId Id of the device for which compilation took place * \param kernelFilename File name containing the kernel * \param preprocessorOptions String containing the preprocessor command-line options used for the - * build \param buildFailed Whether the OpenCL build succeeded + * build + * \param buildFailed Whether the OpenCL build succeeded * * \throws std::bad_alloc if out of memory */ static void writeOclBuildLog(FILE* fplog, diff --git a/src/gromacs/mdlib/calc_verletbuf.h b/src/gromacs/mdlib/calc_verletbuf.h index a013cf2bf9..59b6be9ef3 100644 --- a/src/gromacs/mdlib/calc_verletbuf.h +++ b/src/gromacs/mdlib/calc_verletbuf.h @@ -2,7 +2,7 @@ * This file is part of the GROMACS molecular simulation package. * * Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team. - * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by + * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -112,7 +112,8 @@ VerletbufListSetup verletbufGetSafeListSetup(ListSetupType listType); * \param[in] inputrec The input record * \param[in] nstlist The pair list update frequency in steps (is not taken from \p inputrec) * \param[in] listLifetime The lifetime of the pair-list, usually nstlist-1, but could be different - * for dynamic pruning \param[in] referenceTemperature The reference temperature for the ensemble + * for dynamic pruning + * \param[in] referenceTemperature The reference temperature for the ensemble * \param[in] listSetup The pair-list setup * \returns The computed pair-list radius including buffer */ diff --git a/src/gromacs/mdlib/coupling.h b/src/gromacs/mdlib/coupling.h index 4e8857c3b0..65b5fe74ff 100644 --- a/src/gromacs/mdlib/coupling.h +++ b/src/gromacs/mdlib/coupling.h @@ -266,11 +266,15 @@ void pleaseCiteCouplingAlgorithms(FILE* fplog, const t_inputrec& ir); * the default code path. * * \param[in] kk present value of the kinetic energy of the atoms to be thermalized (in - * arbitrary units) \param[in] sigma target average value of the kinetic energy (ndeg k_b T/2) (in - * the same units as kk) \param[in] ndeg number of degrees of freedom of the atoms to be - * thermalized \param[in] taut relaxation time of the thermostat, in units of 'how often this - * routine is called' \param[in] step the time step this routine is called on \param[in] seed the - * random number generator seed \return the new kinetic energy + * arbitrary units) + * \param[in] sigma target average value of the kinetic energy (ndeg k_b T/2) (in + * the same units as kk) + * \param[in] ndeg number of degrees of freedom of the atoms to be thermalized + * \param[in] taut relaxation time of the thermostat, in units of 'how often this + * routine is called' + * \param[in] step the time step this routine is called on + * \param[in] seed the random number generator seed + * \return the new kinetic energy */ real vrescale_resamplekin(real kk, real sigma, real ndeg, real taut, int64_t step, int64_t seed); diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp index 54915133af..5fad2c1d3f 100644 --- a/src/gromacs/mdlib/sim_util.cpp +++ b/src/gromacs/mdlib/sim_util.cpp @@ -527,7 +527,8 @@ static real averageKineticEnergyEstimate(const t_grpopts& groupOptions) * * \param[in] step The step number, used for checking and printing * \param[in] enerd The energy data; the non-bonded group energies need to be added to - * enerd.term[F_EPOT] before calling this routine \param[in] inputrec The input record + * \c enerd.term[F_EPOT] before calling this routine + * \param[in] inputrec The input record */ static void checkPotentialEnergyValidity(int64_t step, const gmx_enerdata_t& enerd, const t_inputrec& inputrec) { diff --git a/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp b/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp index 84f26a198c..c45ec35cc5 100644 --- a/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp +++ b/src/gromacs/mdtypes/state_propagator_data_gpu_impl_gpu.cpp @@ -206,7 +206,7 @@ std::tuple StatePropagatorDataGpu::Impl::getAtomRangesFromAtomLocality "be All, Local or NonLocal."); } GMX_ASSERT(atomsStartAt >= 0, - "The first elemtnt to copy has negative index. Probably, the GPU propagator state " + "The first element to copy has negative index. Probably, the GPU propagator state " "was not initialized."); GMX_ASSERT(numAtomsToCopy >= 0, "Number of atoms to copy is negative. Probably, the GPU propagator state was not " diff --git a/src/gromacs/nbnxm/nbnxm.h b/src/gromacs/nbnxm/nbnxm.h index b438c9bc33..51b7a4a853 100644 --- a/src/gromacs/nbnxm/nbnxm.h +++ b/src/gromacs/nbnxm/nbnxm.h @@ -326,7 +326,8 @@ public: * The API function for the transformation of the coordinates from one layout to another. * * \param[in] locality Whether coordinates for local or non-local atoms should be - * transformed. \param[in] coordinates Coordinates in plain rvec format to be transformed. + * transformed. + * \param[in] coordinates Coordinates in plain rvec format to be transformed. */ void convertCoordinates(gmx::AtomLocality locality, gmx::ArrayRef coordinates); @@ -373,23 +374,23 @@ public: //! Executes the non-bonded free-energy kernels, local + non-local, always runs on the CPU void dispatchFreeEnergyKernels(const gmx::ArrayRefWithPadding& coords, - gmx::ForceWithShiftForces* forceWithShiftForces, - bool useSimd, - int ntype, - real rlist, - const interaction_const_t& ic, - gmx::ArrayRef shiftvec, - gmx::ArrayRef nbfp, - gmx::ArrayRef nbfp_grid, - gmx::ArrayRef chargeA, - gmx::ArrayRef chargeB, - gmx::ArrayRef typeA, - gmx::ArrayRef typeB, - t_lambda* fepvals, - gmx::ArrayRef lambda, - gmx_enerdata_t* enerd, - const gmx::StepWorkload& stepWork, - t_nrnb* nrnb); + gmx::ForceWithShiftForces* forceWithShiftForces, + bool useSimd, + int ntype, + real rlist, + const interaction_const_t& ic, + gmx::ArrayRef shiftvec, + gmx::ArrayRef nbfp, + gmx::ArrayRef nbfp_grid, + gmx::ArrayRef chargeA, + gmx::ArrayRef chargeB, + gmx::ArrayRef typeA, + gmx::ArrayRef typeB, + t_lambda* fepvals, + gmx::ArrayRef lambda, + gmx_enerdata_t* enerd, + const gmx::StepWorkload& stepWork, + t_nrnb* nrnb); /*! \brief Add the forces stored in nbat to f, zeros the forces in nbat * \param [in] locality Local or non-local diff --git a/src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp b/src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp index 3bde296008..b4b28c0652 100644 --- a/src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp +++ b/src/gromacs/nbnxm/opencl/nbnxm_ocl.cpp @@ -654,7 +654,8 @@ void gpu_launch_kernel(NbnxmGpu* nb, const gmx::StepWorkload& stepWork, const Nb * for OpenCL local memory. * * \param[in] num_threads_z cj4 concurrency equal to the number of threads/work items in the 3-rd - * dimension. \returns the amount of local memory in bytes required by the pruning kernel + * dimension. + * \returns the amount of local memory in bytes required by the pruning kernel */ static inline int calc_shmem_required_prune(const int num_threads_z) { diff --git a/src/gromacs/nbnxm/pairlist.cpp b/src/gromacs/nbnxm/pairlist.cpp index 09338ad44e..cd44bc180a 100644 --- a/src/gromacs/nbnxm/pairlist.cpp +++ b/src/gromacs/nbnxm/pairlist.cpp @@ -121,7 +121,8 @@ static constexpr int jClusterSize() * * \tparam jClusterSize The number of atoms in a j-cluster * \tparam jSubClusterIndex The j-sub-cluster index (0/1), used when size(j-cluster) < - * size(i-cluster) \param[in] ci The i-cluster index + * size(i-cluster) + * \param[in] ci The i-cluster index */ template static inline int cjFromCi(int ci) @@ -158,7 +159,8 @@ static inline int cjFromCi(int ci) * * \tparam layout The pair-list layout * \tparam jSubClusterIndex The j-sub-cluster index (0/1), used when size(j-cluster) < - * size(i-cluster) \param[in] ci The i-cluster index + * size(i-cluster) + * \param[in] ci The i-cluster index */ template static inline int cjFromCi(int ci) diff --git a/src/gromacs/pulling/transformationcoordinate.h b/src/gromacs/pulling/transformationcoordinate.h index c9b6c50119..b8caf90cb8 100644 --- a/src/gromacs/pulling/transformationcoordinate.h +++ b/src/gromacs/pulling/transformationcoordinate.h @@ -59,7 +59,8 @@ class ArrayRef; * This requires the values of the pull coordinates of lower indices to be set * \param[in] coord The (transformation) coordinate to compute the value for * \param[in] variableCoords Pull coordinates used as variables, entries 0 to coord->coordIndex - * will be used \returns Transformation value for pull coordinate. + * will be used + * \returns Transformation value for pull coordinate. */ double getTransformationPullCoordinateValue(pull_coord_work_t* coord, ArrayRef variableCoords); diff --git a/src/gromacs/taskassignment/decidegpuusage.h b/src/gromacs/taskassignment/decidegpuusage.h index 76b6f40042..693804efd1 100644 --- a/src/gromacs/taskassignment/decidegpuusage.h +++ b/src/gromacs/taskassignment/decidegpuusage.h @@ -243,7 +243,8 @@ bool decideWhetherToUseGpusForPme(bool useGpuForNonbonded, * * \param[in] useGpuForPme PME task assignment, true if PME task is mapped to the GPU. * \param[in] pmeFftTarget The user's choice for -pmefft for where to assign the FFT - * work of the PME task. \param[in] inputrec The user input record + * work of the PME task. + * \param[in] inputrec The user input record * */ PmeRunMode determinePmeRunMode(bool useGpuForPme, const TaskTarget& pmeFftTarget, const t_inputrec& inputrec); -- 2.22.0